Implicating type 2 diabetes effector genes in relevant metabolic cellular models using promoter-focused Capture-C.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39240351", "kind": "science-record", "revision": 2, "content_hash": "sha256:55be34e8b097db62762fa476ead3d2133449001a3942e3e787d98cc389d21112", "created_at": "2026-11-01T20:29:22Z", "updated_at": "2026-11-01T21:33:50Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Implicating type 2 diabetes effector genes in relevant metabolic cellular models using promoter-focused Capture-C.", "doi": "10.1007/s00125-024-06261-x", "pmid": "39240351", "authors": ["Nicholas A Wachowski", "James A Pippin", "Keith Boehm", "Sumei Lu", "Michelle E Leonard", "Elisabetta Manduchi", "Ursula W Parlin", "Martin Wabitsch", "Alessandra Chesi", "Andrew D Wells", "Struan F A Grant", "Matthew C Pahl"], "journal": "Diabetologia", "year": 2024, "abstract": "AIMS/HYPOTHESIS: Genome-wide association studies (GWAS) have identified hundreds of type 2 diabetes loci, with the vast majority of signals located in non-coding regions; as a consequence, it remains largely unclear which 'effector' genes these variants influence. Determining these effector genes has been hampered by the relatively challenging cellular settings in which they are hypothesised to confer their effects.\nMETHODS: To implicate such effector genes, we elected to generate and integrate high-resolution promoter-focused Capture-C, assay for transposase-accessible chromatin with sequencing (ATAC-seq) and RNA-seq datasets to characterise chromatin and expression profiles in multiple cell lines relevant to type 2 diabetes for subsequent functional follow-up analyses: EndoC-BH1 (pancreatic beta cell), HepG2 (hepatocyte) and Simpson-Golabi-Behmel syndrome (SGBS; adipocyte).\nRESULTS: The subsequent variant-to-gene analysis implicated 810 candidate effector genes at 370 type 2 diabetes risk loci. Using partitioned linkage disequilibrium score regression, we observed enrichment for type 2 diabetes and fasting glucose GWAS loci in promoter-connected putative cis-regulatory elements in EndoC-BH1 cells as well as fasting insulin GWAS loci in SGBS cells. Moreover, as a proof of principle, when we knocked down expression of the SMCO4 gene in EndoC-BH1 cells, we observed a statistically significant increase in insulin secretion.\nCONCLUSIONS/INTERPRETATION: These results provide a resource for comparing tissue-specific data in tractable cellular models as opposed to relatively challenging primary cell settings.\nDATA AVAILABILITY: Raw and processed next-generation sequencing data for EndoC-BH1, HepG2, SGBS_undiff and SGBS_diff cells are deposited in GEO under the Superseries accession GSE262484. Promoter-focused Capture-C data are deposited under accession GSE262496. Hi-C data are deposited under accession GSE262481. Bulk ATAC-seq data are deposited under accession GSE262479. Bulk RNA-seq data are deposited under accession GSE262480.", "claims": [{"id": "claim-method", "statement": "To this end, we performed partitioned LD score regression [30] to test for enrichment of putative cREs (promoter OCRs + PIR-OCRs) (Fig. 3, ESM Table 4).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39240351", "locator": "sections[15] \"Variant-to-gene mapping in metabolic-relevant cells and prioritisation of type 2 diabetes-associated GWAS signals\" paragraph 2", "quote": "To this end, we performed partitioned LD score regression [30] to test for enrichment of putative cREs (promoter OCRs + PIR-OCRs) (Fig. 3, ESM Table 4)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Raw and processed next-generation sequencing data for EndoC-BH1, HepG2, SGBS_undiff and SGBS_diff cells are deposited in GEO under the Superseries accession GSE262484. Promoter-focused Capture-C data are deposited under accession GSE262496. 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Bulk RNA-seq data are deposited under accession GSE262480."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The subsequent variant-to-gene analysis implicated 810 candidate effector genes at 370 type 2 diabetes risk loci.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39240351", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "The subsequent variant-to-gene analysis implicated 810 candidate effector genes at 370 type 2 diabetes risk loci."}, {"asset": "source:pmid:39240351", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Using partitioned linkage disequilibrium score regression, we observed enrichment for type 2 diabetes and fasting glucose GWAS loci in promoter-connected putative cis-regulatory elements in EndoC-BH1 cells as well as fasting insulin GWAS loci in SGBS cells."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The subsequent variant-to-gene analysis implicated 810 candidate effector genes at 370 type 2 diabetes risk loci.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:39240351"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE262479"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE262479"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39240351", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1007/s00125-024-06261-x", "sha256": "sha256:e1cea6c0b34a61b00e711bfed6dd0131980a606dc804368dff37a25ca57f48a8", "bytes": 53769, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1007/s00125-024-06261-x", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11604697", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE262479", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE262479", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE262479", "version": null, "note": "Raw and processed next-generation sequencing data for EndoC-BH1, HepG2, SGBS_undiff and SGBS_diff cells are deposited in GEO under the Superseries accession GSE262484. 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See the electroni", "the manufacturer’s instructions: Cells were passaged when confluence was observed or otherwise pa"], "order_basis": "paper_text_order:887", "id": "assay:3"}, {"role": "data_generation", "definition_id": "amplicon_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["ttings. DATA AVAILABILITY: Raw and processed next-generation sequencing data for EndoC-BH1, HepG2, SGBS_undiff and S"], "order_basis": "paper_text_order:1738", "id": "assay:4"}, {"role": "analysis", "definition_id": "genetic_association", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["gwas_locus_scan"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["Genome-wide association studies"], "order_basis": "consumes_earlier_output", "id": "assay:5"}]}